The drawn-out battle about a transportation finance bill appears to have hit a new snag: tolls.

Legislators passed a transportation funding package Wednesday that would raise up to $805 million in new annual revenue for the state Department of Transportation by 2018. But Governor Deval Patrick said that he would not sign the bill in its current form, because the funding promised in the bill includes revenue from tolls that could disappear in the next few years.

Starting in 2017, tolls on the Massachusetts Turnpike will no longer be legally mandated. If the tolls are eliminated, the lost revenue could leave the state’s transportation system with as much as $130 million less than projected in the bill.

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In a statement, Patrick said he would send the bill back to lawmakers with an amendment intended to ensure that the Transportation Department is not left out to dry.

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House Speaker Robert A. DeLeo said he was “somewhat surprised” by the governor’s objections and did not agree with the administration’s assertion that the bill does not provide as much new revenue as it promises.

“I’m anxious to see exactly what amendments he wants to file and what the issues are, because I think we’re there,” DeLeo said. “Bottom line: The numbers are solid.”

Transportation Secretary Richard A. Davey said he met with legislators in recent weeks to outline a need for a fix. In a June 6 memo to the legislators, he suggested two solutions: vote to continue the tolls past 2017 or raise the gas tax.

“This shouldn’t be a surprise to anyone,” Davey said. “It’s clear this was our deepest concern.”

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But DeLeo said Davey raised concerns too late.

“The bill was done,” he said. “This was not even brought to our attention until after we had completed negotiations.”

Patrick has 10 days to return the bill with the amendment. After that, legislators will vote on whether to approve it. The legislation approved Wednesday passed both chambers with veto-proof margins.

The transportation funding package relies on a mish-mash of funding sources — a 3-cent gas tax, a $1 cigarette tax, a tax on computer software and utilities, money diverted from an underground storage cleanup fund — to deliver an average of $600 million per year over the next five years to help put the state’s transit agencies on firm financial footing.

Still, it is far short of the $1 billion proposal put forth by Patrick early this year, but will help regional transit authorities pay their operating costs in advance, allow MassDOT to pay for personnel costs without borrowing money, and will close the MBTA’s budget deficit.

Without a funding plan in place, the T’s budget will be in financial limbo, because its fiscal year starts Monday. Davey said the T will continue to take a wait-and-see approach in coming weeks, holding off on fare hikes or service cuts for at least a couple of months.

“We’re not going to panic; we’re not going to create a crisis,” Davey said. When it comes to enacting fare increases, he continued, “we don’t want to go there.”

Stephanie Pollack, associate director of Northeastern University’s Dukakis Center for Urban and Regional Policy, said Patrick’s issue with tolls is an important one.

“You’ve got to shore up every last dollar,” Pollack said. “I know we’re down to the last minute, but it feels like it would still be great if we could make one last run at getting everything exactly right.”

Marc Draisen, executive director of the Metropolitan Area Planning Council, said he disagreed that the amendment was essential and said it could be addressed by legislators in a year or two.

“Getting $600 million for your program is not something that happens every day,” said Draisen. “I know it’s not everything we want, and it’s not everything we need, but it’s 60 percent, and that’s a pretty good year’s work.”